Multiple peptides EIC chromatograms display value

Multiple peptides EIC chromatograms display value Juan C. Rojas E.  2021-09-03

Hi all,

A colleague has performed a scheduled PRM, including a full ms scan in each cycle. Then he has created a Skyline project to analyze the targets both at the precursor and fragment level. Now we have a question about the y-axis values displayed when the EIC chromatograms of multiple peptides are displayed (when you highight a peptide list or a protein) as in the image attached. Are the values the summed intensity of all transitions? Precursor or fragment transitions? Is it only the intensity of the highest transition?

I hope all is going well and hope to hear back from you.

Nick Shulman responded:  2021-09-03
Yes, the chromatograms are obtained by summing the intensities of the chromatograms of all of the transitions across all of the precursors belonging to that peptide.
All of the transitions (precursors, products, quantitative, non-quantitative) are always included in terms of summing transitions to make the peptide-level chromatograms.
-- Nick